[Genome] use of the shortmatch track through an url

[Robert Castelo]

Heather,

thanks a lot, this is exactly what i was looking for.

best regards,

robert.

On Wed, 2007-07-04 at 05:28 -0700, Heather Trumbower wrote:
> Hi Robert:
> 
> The genome browser URL recognizes a good number of key/value pairs.
> To open to a particular database and region, you use db= and position=.
> For example:
> 
> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr22:15000000-16000000
> 
> You can also control the visibility of any track.   The value is simply 
> 'full', 'pack', 'squish', 'dense' or 'hide'.  The key can be found by 
> looking at the track label (it is a link to the hgTrackUi configuration 
> page) or by doing http://genome.ucsc.edu/cgi-bin/cartDump.
> 
> The key for the Short Match track is oligoMatch.
> 
> So now your URL looks like:
> 
> http://genome.ucsc.edu/cgi-bin/hgTracks?oligoMatch=full&db=hg17&position=chr22:15000000-16000000
> 
> The last thing you would want to set is the search string.   We keep that 
> in the key hgt.oligoMatch:
> 
> http://genome.ucsc.edu/cgi-bin/hgTracks?hgt.oligoMatch=ccccc&oligoMatch=full&db=hg17&position=chr22:15000000-16000000
> 
> I hope this is what you are looking for, let us know if you have further 
> questions.
> 
> Heather Trumbower
> UCSC Genome Bioinformatics Group
> 
> 
>   On Tue, 3 Jul 2007, Robert Castelo wrote:
> 
> > dear people at ucsc,
> >
> > i'd like to ask you if it is possible to use the Short Match track under
> > the Mapping and Sequencing Tracks directly through an url such that i
> > can build a link which, when i click on it, opens the genome browser on
> > a particular region of the genome and showing the perfect matches to
> > some short sequence of my interest (i.e., the short sequence would have
> > to go written on the url somehow..)
> >
> > i know this could be worked out through a custom track but i was
> > wondering whether the Short Match would do this job also for me.
> >
> >
> > thanks!!
> >
> > robert.
> >
> >
>